The charity workers were conducting "administrative tasks," including a visit to a new school opening, the NGO said in a statement on Friday.
The charity said there have been no ransom demands so far, and that French and Iraqi authorities are currently coordinating an investigation to find them.
"They disappeared between two meetings. They were on a mission authorized by the French Embassy," Jeanne der Agopian, spokesperson for SOS Chrtiens d'Orient, told CNN.
According to the agency, the employees were expected to drive to an appointment on Monday afternoon.
After several unsuccessful attempts to contact the aid workers on Tuesday, SOS Chrtiens d'Orient alerted the French authorities on Wednesday.
SOS Chrtiens d'Orient's mission is to help Christians in the region. The organization added the missing had a "thorough knowledge of the crisis areas" and "followed a security protocol adapted for the region."
In December, a French journalist was kidnapped close to the U.S. embassy in Baghdad but was released 24 hours later.
CNN's Amy Woodyatt contributed to this report.